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From: "Thorsten Schweikardt" thorsten@mail.uni-mainz.de To: modeller_usage@salilab.org Subject: More weight for user distance restraints Date: Thu, 28 Aug 2003 16:28:34 +0200

Hi to all,

I have a problem with user defined distance restraints, I want to model the n-terminus of a protein that's available as pdb with the help of measured distances. So far, it works, but one little problem remains: the distance-requirements are not met entirely, because modeller does not distort the rest of the protein at all, is there a possibility to force it to add more weight to these distance restraints, even if it means distorting the template protein?

Thanks, Thorsten University of Mainz

My Top-File: ----------------------------- INCLUDE SET ALNFILE = 'alignment.ali' SET KNOWNS = 'protein1' SET SEQUENCE = 'protein1plusnterm' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL= 1 SET ENDING_MODEL = 20 SET LIBRARY_SCHEDULE = 4 SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS = 'OG:3' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 10.0 SET ATOM_IDS = 'OG:116' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 0.0 SET ATOM_IDS = 'CA:42' 'CA:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 1.0 SET ATOM_IDS = 'CA:3' 'CA:42' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 21.0 4.0 SET ATOM_IDS = 'CA:3' 'CA:116' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 50.0 1.0 RETURN END_SUBROUTINE

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